Unraveling the Acidithiobacillus caldus complete genome and its central metabolisms for carbon assimilation
Introduction
Acidithiobacillus caldus, a moderately thermoacidophilic and obligately chemolithotrophic r-Proteobacterium with an optimal growth temperature of 40–45°C and pH of 2–2.5 (Kelly and Wood, 2002), was reported to be the dominant sulfur-oxidizing bacterium in biomining (Xia et al., 2009, Zhou et al., 2009, Zeng et al., 2010, Spolaore et al., 2011) and it was also found to be associated with acid mine drainage (Kamimura et al., 2010). The main roles of A. caldus in biomining processes include: 1) to oxidize elemental sulfur and reduced inorganic sulfur compounds (RISCs), thus produces the acidity that is essential for biomining and 2) to remove the accumulated elemental sulfur that would otherwise retard the oxidation of ores (Dopson and Lindström, 1999, Watling, 2006). RISC oxidation has been the focus of A. caldus investigations (Mangold et al., 2011). It was shown that RISC oxidation in A. caldus is coupled to ATP generation via electron transport phosphorylation (Dopson et al., 2002). A periplasmic tetrathionate hydrolase (TetH) was purified and characterized from A. caldus (Bugaytsova and Lindström, 2004). The TetH gene was cloned and co-transcribed with a thiosulfate quinone oxidoreductase gene (doxD) from a common genetic cluster in A. caldus (Rzhepishevska et al., 2007). Further, a gene encoding a sulfur oxygenase reductase that oxidizes elemental sulfur was identified in A. caldus (Chen et al., 2007).
Comparing to the knowledge of RISC oxidation and energy metabolism, much less was done to study CO2 fixation and central metabolism of carbon compounds in A. caldus in the past years. Uptake and fixation of CO2 at an extremely acidic condition has been much overlooked until recently a form II Rubisco was presented in Acidithiobacillus ferrooxidans that could promote the ability to fix CO2 at different concentrations of CO2 (Esparza et al., 2010). Considering the extremely low pH (thus CO2 would be existing mainly as dissolved gas instead of bicarbonates), as well as the oligotrophic nature of the environments in which Acidithiobacillus species lives, it was expected that Acidithiobacillus species might possess novel strategies to sequestrate carbon compounds from environments for growth.
In this report, we present the complete genome sequence of A. caldus SM-1, which was isolated from a pilot bioleaching reactor (Liu et al., 2010). Genome analysis was focused on the central metabolisms for carbon compounds and the results were validated by applying proteomic tools. We concluded that SM-1 was able to uptake and assimilate a variety of organic compounds for growth.
Section snippets
Preparation of genomic DNA and DNA sequencing
A. caldus SM-1 was cultivated at 45°C in 9 K medium (Silverman and Lundgren, 1959) supplemented with 2% elemental sulfur and 0.05% yeast extract. Cells were harvested in the stable-phase and sulfur was removed from the cells by differential centrifugation. Genomic DNA was extracted by phenol–chloroform methods as described previously (Marmur, 1961).
The A. caldus SM-1 genome was sequenced by using the Roche 454 Genome Sequencer FLX instrument (454 Life Science, Branford, USA). A total of 522,895
General features of the A. caldus SM-1 genome
The complete SM-1 genome was composed of one chromosome and four plasmids (pLAtc1, pLAtc1, pLAtc3, and pLAtcm), giving a total genome size of 3,237,599 bp (Fig. 1 and Table 1). The circular chromosome comprised 91% of the genome with an average GC content of 61%. There were 2880 putative ORFs, of which 1938 ORFs could be functionally annotated, 744 were conserved hypothetical proteins while 198 were unique hypothetical proteins. Six hundred and five (21%) ORFs were predicted as secretory
Discussion
The occurrence of large numbers of transposons can result in genome instability, as reported for the Acetobacter pasteurianus genome (Azuma et al., 2009). The SM-1 strain encodes 198 transposable genetic elements including 37 copies of ISAtc1 and 12 copies of ISAtfe. Based on our analysis, these transposable genetic elements have exerted significant effects on the SM-1 genome stability including gene inactivation, gene loss and gene acquisition: seven genes were interrupted by insertion of a
Acknowledgements
The work was supported by the National Science Foundation of China (No. 30870039) and the National Basic Research Program of China (973 Program, No. 2010CB630903). Constructive suggestion during preparation of the manuscript from Prof. Y. Tao at Institute of Microbiology, Chinese Academy of Sciences is highly acknowledged.
References (25)
- et al.
Toward the complete membrane proteome: high coverage of integral membrane proteins through transmembrane peptide detection
Mol. Cell. Proteomics
(2006) - et al.
Analysis of iron- and sulfur-oxidizing bacteria in a treatment plant of acid rock drainage from a Japanese pyrite mine by use of ribulose-1, 5-bisphosphate carboxylase/oxygenase large-subunit gene
J. Biosci. Bioeng.
(2010) The bioleaching of sulphide minerals with emphasis on copper sulphides: a review
Hydrometalllurgy
(2006)- et al.
Bioleaching of chalcopyrite concentrate by a moderately thermophilic culture in a stirred tank reactor
Bioresour. Technol.
(2009) - et al.
Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus
Nucleic Acid Res.
(2009) - et al.
Localization, purification and properties of a tetrathionate hydrolase from Acidithiobacillus caldus
Eur. J. Biochem.
(2004) - et al.
Novel bacterial sulfur oxygenase reductases from bioreactors treating gold-bearing concentrates
Appl. Microbiol. Biotechnol.
(2007) - et al.
Identifying bacterial genes and endosymbiont DNA with Glimmer
Bioinformatics
(2007) - et al.
Potential role of Thiobacillus caldus in arenopyrite bioleaching
Appl. Environ. Microbiol.
(1999) - et al.
ATP generation during reduced inorganic sulfur compound oxidation by Acidithiobacillus caldus is exclusively due to electron transport phosphorylation
Extremophiles
(2002)
Characteristics of attachment and growth of Thiobacillus caldus on sulphide minerals: a chemotactic response to sulphur minerals?
Environ. Microbiol.
Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, carbon fixation in A. ferrooxidans
BMC Microbiol.
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